Multiple sequence alignment - TraesCS1A01G211800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G211800 chr1A 100.000 2307 0 0 1 2307 374279937 374277631 0.000000e+00 4261.0
1 TraesCS1A01G211800 chr1A 100.000 245 0 0 2761 3005 374277177 374276933 1.270000e-123 453.0
2 TraesCS1A01G211800 chr1D 93.470 2236 90 23 106 2304 300027183 300024967 0.000000e+00 3269.0
3 TraesCS1A01G211800 chr1D 91.667 72 3 1 1 72 300027254 300027186 2.470000e-16 97.1
4 TraesCS1A01G211800 chr1B 92.369 2241 99 23 1 2195 404899553 404897339 0.000000e+00 3125.0
5 TraesCS1A01G211800 chr1B 94.017 117 7 0 2773 2889 404897272 404897156 8.560000e-41 178.0
6 TraesCS1A01G211800 chr6D 94.444 36 2 0 1705 1740 464674913 464674878 4.180000e-04 56.5
7 TraesCS1A01G211800 chr6B 94.444 36 2 0 1705 1740 708516288 708516253 4.180000e-04 56.5
8 TraesCS1A01G211800 chr6A 94.444 36 2 0 1705 1740 611197770 611197805 4.180000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G211800 chr1A 374276933 374279937 3004 True 2357.00 4261 100.0000 1 3005 2 chr1A.!!$R1 3004
1 TraesCS1A01G211800 chr1D 300024967 300027254 2287 True 1683.05 3269 92.5685 1 2304 2 chr1D.!!$R1 2303
2 TraesCS1A01G211800 chr1B 404897156 404899553 2397 True 1651.50 3125 93.1930 1 2889 2 chr1B.!!$R1 2888

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
982 1015 0.033601 TGCCTTGTGTGTGGGAGTTT 60.034 50.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2100 0.179089 ATCTGAGCACATCTGGCGAC 60.179 55.0 0.0 0.0 36.08 5.19 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.236586 GTCTTCTTTCCAAAAACAAAAGCAAAT 58.763 29.630 0.00 0.00 31.55 2.32
78 79 1.367599 GACGACGGAGACACGAGGAT 61.368 60.000 0.00 0.00 37.61 3.24
95 96 1.416401 GGATACGCCTCAAGGAATCCA 59.584 52.381 0.61 0.00 38.92 3.41
135 136 1.067142 TCGTGGCACCAAGATAGACAC 60.067 52.381 12.86 0.00 30.07 3.67
150 151 5.532779 AGATAGACACACATTCAGAGCGATA 59.467 40.000 0.00 0.00 0.00 2.92
330 333 7.274686 ACACGCACAGCCAATAAATAAATAAAC 59.725 33.333 0.00 0.00 0.00 2.01
348 351 4.330944 AAACAATTTCCCCCGAGTTTTC 57.669 40.909 0.00 0.00 0.00 2.29
457 460 1.449601 CGTAACTCCCGCCAGCAAT 60.450 57.895 0.00 0.00 0.00 3.56
458 461 0.179094 CGTAACTCCCGCCAGCAATA 60.179 55.000 0.00 0.00 0.00 1.90
461 464 0.676782 AACTCCCGCCAGCAATACAC 60.677 55.000 0.00 0.00 0.00 2.90
523 529 2.094417 CCAAAAAGCCGACGATCTTCTC 59.906 50.000 0.00 0.00 0.00 2.87
548 554 1.781786 TGCCAGTTTTACAGCCCAAA 58.218 45.000 0.00 0.00 0.00 3.28
574 580 2.494504 CTTCGGTTTCGTGGCGCTTC 62.495 60.000 7.64 0.00 37.69 3.86
613 619 2.135933 CGAGCAGTTAATTCCCCGATC 58.864 52.381 0.00 0.00 0.00 3.69
630 636 0.601841 ATCCTTCGGTTTTGCGACGT 60.602 50.000 0.00 0.00 0.00 4.34
631 637 1.083015 CCTTCGGTTTTGCGACGTG 60.083 57.895 0.00 0.00 0.00 4.49
632 638 1.492319 CCTTCGGTTTTGCGACGTGA 61.492 55.000 0.00 0.00 0.00 4.35
633 639 0.302288 CTTCGGTTTTGCGACGTGAA 59.698 50.000 0.00 0.00 0.00 3.18
634 640 0.725686 TTCGGTTTTGCGACGTGAAA 59.274 45.000 0.00 0.00 0.00 2.69
671 677 1.269448 TCTGCCTTGTTTTCGATTGCC 59.731 47.619 0.00 0.00 0.00 4.52
706 713 1.400494 GCTGCGTATTTAAGTGTGGGG 59.600 52.381 0.00 0.00 0.00 4.96
823 840 1.867363 TTAAGCTCCCCACTCTCTCC 58.133 55.000 0.00 0.00 0.00 3.71
842 860 0.814457 CTCCTCTTCCACCTCTCACG 59.186 60.000 0.00 0.00 0.00 4.35
879 897 0.539986 TTCCCCGTTGGACTATCAGC 59.460 55.000 0.00 0.00 45.11 4.26
910 943 1.373873 GAGCAAGCAAGCAAAGCCC 60.374 57.895 3.19 0.00 36.85 5.19
928 961 1.499056 CGCAAGCTGCTCGTGATTT 59.501 52.632 1.00 0.00 42.25 2.17
937 970 3.181507 GCTGCTCGTGATTTCAAGCATTA 60.182 43.478 7.25 0.00 38.55 1.90
943 976 5.113383 TCGTGATTTCAAGCATTACGGTAT 58.887 37.500 0.00 0.00 35.09 2.73
974 1007 0.467844 TGCTCCATTGCCTTGTGTGT 60.468 50.000 0.00 0.00 0.00 3.72
975 1008 0.038892 GCTCCATTGCCTTGTGTGTG 60.039 55.000 0.00 0.00 0.00 3.82
979 1012 0.599558 CATTGCCTTGTGTGTGGGAG 59.400 55.000 0.00 0.00 0.00 4.30
982 1015 0.033601 TGCCTTGTGTGTGGGAGTTT 60.034 50.000 0.00 0.00 0.00 2.66
995 1028 1.531578 GGGAGTTTGTCTTGCTCGTTC 59.468 52.381 0.00 0.00 0.00 3.95
1191 1224 1.227674 GGATGGTAAGCCGGCTCAG 60.228 63.158 32.93 0.00 37.67 3.35
1239 1272 2.496817 GATCCCGCGAGAAGCTGT 59.503 61.111 8.23 0.00 45.59 4.40
1570 1603 1.353804 GAGCAAAACAACGACGGCA 59.646 52.632 0.00 0.00 0.00 5.69
1698 1731 0.523072 CATGCAAGAAGGTGTTCCGG 59.477 55.000 0.00 0.00 39.05 5.14
2016 2070 1.069823 AGACAGTGAGGTCAGCTGTTG 59.930 52.381 14.67 4.94 40.29 3.33
2021 2075 0.829990 TGAGGTCAGCTGTTGTGACA 59.170 50.000 14.67 5.41 45.24 3.58
2033 2087 0.884259 TTGTGACATGTGACCAGCCG 60.884 55.000 13.12 0.00 0.00 5.52
2046 2100 3.518998 AGCCGTCGTCCAGATCGG 61.519 66.667 0.00 0.00 42.40 4.18
2100 2155 3.880846 GCCCAGCTTCGGCAATCG 61.881 66.667 15.40 0.00 46.27 3.34
2118 2173 0.038618 CGGCATGCATGGATGGATTG 60.039 55.000 27.34 4.89 36.67 2.67
2119 2174 1.045407 GGCATGCATGGATGGATTGT 58.955 50.000 27.34 0.00 36.67 2.71
2213 2268 8.608844 TTTTTGCCTTTTCTTTTCAGTTACAA 57.391 26.923 0.00 0.00 0.00 2.41
2283 2339 5.390613 CCGAATCATTTTTGTCCACTGTAC 58.609 41.667 0.00 0.00 0.00 2.90
2284 2340 5.049060 CCGAATCATTTTTGTCCACTGTACA 60.049 40.000 0.00 0.00 0.00 2.90
2285 2341 5.851177 CGAATCATTTTTGTCCACTGTACAC 59.149 40.000 0.00 0.00 0.00 2.90
2286 2342 6.293407 CGAATCATTTTTGTCCACTGTACACT 60.293 38.462 0.00 0.00 0.00 3.55
2305 2361 9.386010 TGTACACTTACATGTTACTCTGTTTTT 57.614 29.630 2.30 0.00 32.98 1.94
2833 2889 4.211374 CGCTTTGCTGAACTTTACAGTAGT 59.789 41.667 0.00 0.00 37.64 2.73
2834 2890 5.404366 CGCTTTGCTGAACTTTACAGTAGTA 59.596 40.000 0.00 0.00 37.64 1.82
2836 2892 6.645415 GCTTTGCTGAACTTTACAGTAGTAGA 59.355 38.462 0.00 0.00 37.64 2.59
2852 2908 5.773680 AGTAGTAGAAACAGCTCACCACTTA 59.226 40.000 0.00 0.00 0.00 2.24
2870 2926 0.601576 TAAGCTCGCGAAACTGCCAA 60.602 50.000 11.33 0.00 0.00 4.52
2881 2937 2.035530 AACTGCCAATGCTCTAGCTC 57.964 50.000 3.26 0.00 42.66 4.09
2889 2945 4.874966 GCCAATGCTCTAGCTCCTATAATG 59.125 45.833 3.26 0.00 42.66 1.90
2890 2946 4.874966 CCAATGCTCTAGCTCCTATAATGC 59.125 45.833 3.26 0.00 42.66 3.56
2891 2947 5.338219 CCAATGCTCTAGCTCCTATAATGCT 60.338 44.000 3.26 0.00 42.66 3.79
2892 2948 4.797800 TGCTCTAGCTCCTATAATGCTG 57.202 45.455 3.26 0.00 42.66 4.41
2893 2949 4.411013 TGCTCTAGCTCCTATAATGCTGA 58.589 43.478 3.26 0.00 42.66 4.26
2894 2950 4.835056 TGCTCTAGCTCCTATAATGCTGAA 59.165 41.667 3.26 0.00 42.66 3.02
2895 2951 5.167845 GCTCTAGCTCCTATAATGCTGAAC 58.832 45.833 0.00 0.00 37.62 3.18
2896 2952 5.279206 GCTCTAGCTCCTATAATGCTGAACA 60.279 44.000 0.00 0.00 37.62 3.18
2897 2953 6.338214 TCTAGCTCCTATAATGCTGAACAG 57.662 41.667 0.00 0.00 37.62 3.16
2898 2954 5.835819 TCTAGCTCCTATAATGCTGAACAGT 59.164 40.000 0.00 0.00 37.62 3.55
2899 2955 5.365021 AGCTCCTATAATGCTGAACAGTT 57.635 39.130 3.77 0.00 35.54 3.16
2900 2956 5.121811 AGCTCCTATAATGCTGAACAGTTG 58.878 41.667 0.00 0.00 35.54 3.16
2901 2957 5.104776 AGCTCCTATAATGCTGAACAGTTGA 60.105 40.000 0.00 0.00 35.54 3.18
2902 2958 5.586243 GCTCCTATAATGCTGAACAGTTGAA 59.414 40.000 0.00 0.00 0.00 2.69
2903 2959 6.261826 GCTCCTATAATGCTGAACAGTTGAAT 59.738 38.462 0.00 0.00 0.00 2.57
2904 2960 7.442364 GCTCCTATAATGCTGAACAGTTGAATA 59.558 37.037 0.00 0.00 0.00 1.75
2905 2961 8.893219 TCCTATAATGCTGAACAGTTGAATAG 57.107 34.615 0.00 6.57 0.00 1.73
2906 2962 8.486210 TCCTATAATGCTGAACAGTTGAATAGT 58.514 33.333 0.00 0.00 0.00 2.12
2907 2963 8.768955 CCTATAATGCTGAACAGTTGAATAGTC 58.231 37.037 0.00 0.00 0.00 2.59
2908 2964 5.536554 AATGCTGAACAGTTGAATAGTCG 57.463 39.130 0.00 0.00 0.00 4.18
2909 2965 4.251543 TGCTGAACAGTTGAATAGTCGA 57.748 40.909 0.00 0.00 0.00 4.20
2910 2966 4.627058 TGCTGAACAGTTGAATAGTCGAA 58.373 39.130 0.00 0.00 0.00 3.71
2911 2967 5.237815 TGCTGAACAGTTGAATAGTCGAAT 58.762 37.500 0.00 0.00 0.00 3.34
2912 2968 6.394809 TGCTGAACAGTTGAATAGTCGAATA 58.605 36.000 0.00 0.00 0.00 1.75
2913 2969 6.531594 TGCTGAACAGTTGAATAGTCGAATAG 59.468 38.462 0.00 0.00 0.00 1.73
2914 2970 6.531948 GCTGAACAGTTGAATAGTCGAATAGT 59.468 38.462 0.00 0.00 0.00 2.12
2915 2971 7.063544 GCTGAACAGTTGAATAGTCGAATAGTT 59.936 37.037 0.00 0.00 0.00 2.24
2916 2972 8.239681 TGAACAGTTGAATAGTCGAATAGTTG 57.760 34.615 0.00 0.00 0.00 3.16
2917 2973 6.648725 ACAGTTGAATAGTCGAATAGTTGC 57.351 37.500 0.00 0.00 0.00 4.17
2918 2974 6.163476 ACAGTTGAATAGTCGAATAGTTGCA 58.837 36.000 0.00 0.00 0.00 4.08
2919 2975 6.649141 ACAGTTGAATAGTCGAATAGTTGCAA 59.351 34.615 0.00 0.00 0.00 4.08
2920 2976 7.172532 ACAGTTGAATAGTCGAATAGTTGCAAA 59.827 33.333 0.00 0.00 0.00 3.68
2921 2977 8.015087 CAGTTGAATAGTCGAATAGTTGCAAAA 58.985 33.333 0.00 0.00 0.00 2.44
2922 2978 8.015658 AGTTGAATAGTCGAATAGTTGCAAAAC 58.984 33.333 0.00 0.00 0.00 2.43
2923 2979 6.837992 TGAATAGTCGAATAGTTGCAAAACC 58.162 36.000 0.00 0.00 0.00 3.27
2924 2980 6.653320 TGAATAGTCGAATAGTTGCAAAACCT 59.347 34.615 0.00 0.00 0.00 3.50
2925 2981 7.820386 TGAATAGTCGAATAGTTGCAAAACCTA 59.180 33.333 0.00 0.00 0.00 3.08
2926 2982 8.556213 AATAGTCGAATAGTTGCAAAACCTAA 57.444 30.769 0.00 0.00 0.00 2.69
2927 2983 6.870971 AGTCGAATAGTTGCAAAACCTAAA 57.129 33.333 0.00 0.00 0.00 1.85
2928 2984 6.665465 AGTCGAATAGTTGCAAAACCTAAAC 58.335 36.000 0.00 0.00 0.00 2.01
2929 2985 6.485648 AGTCGAATAGTTGCAAAACCTAAACT 59.514 34.615 0.00 0.00 36.80 2.66
2930 2986 6.577427 GTCGAATAGTTGCAAAACCTAAACTG 59.423 38.462 0.00 0.00 34.76 3.16
2931 2987 6.261381 TCGAATAGTTGCAAAACCTAAACTGT 59.739 34.615 0.00 0.00 34.76 3.55
2932 2988 6.915843 CGAATAGTTGCAAAACCTAAACTGTT 59.084 34.615 0.00 0.00 36.89 3.16
2933 2989 7.096640 CGAATAGTTGCAAAACCTAAACTGTTG 60.097 37.037 0.00 0.00 35.11 3.33
2934 2990 5.400066 AGTTGCAAAACCTAAACTGTTGT 57.600 34.783 0.00 0.00 31.82 3.32
2935 2991 5.789521 AGTTGCAAAACCTAAACTGTTGTT 58.210 33.333 0.00 0.00 38.16 2.83
2936 2992 5.637387 AGTTGCAAAACCTAAACTGTTGTTG 59.363 36.000 0.00 0.00 36.39 3.33
2937 2993 4.499183 TGCAAAACCTAAACTGTTGTTGG 58.501 39.130 0.00 0.00 36.39 3.77
2938 2994 3.308595 GCAAAACCTAAACTGTTGTTGGC 59.691 43.478 0.00 0.00 36.39 4.52
2939 2995 3.812156 AAACCTAAACTGTTGTTGGCC 57.188 42.857 0.00 0.00 36.39 5.36
2940 2996 2.445682 ACCTAAACTGTTGTTGGCCA 57.554 45.000 0.00 0.00 36.39 5.36
2941 2997 2.028876 ACCTAAACTGTTGTTGGCCAC 58.971 47.619 3.88 0.75 36.39 5.01
2942 2998 1.001815 CCTAAACTGTTGTTGGCCACG 60.002 52.381 3.88 0.00 36.39 4.94
2943 2999 1.001815 CTAAACTGTTGTTGGCCACGG 60.002 52.381 3.88 0.48 36.39 4.94
2944 3000 0.968393 AAACTGTTGTTGGCCACGGT 60.968 50.000 3.88 1.30 36.39 4.83
2945 3001 1.662438 AACTGTTGTTGGCCACGGTG 61.662 55.000 3.88 0.00 34.71 4.94
2946 3002 2.044848 TGTTGTTGGCCACGGTGT 60.045 55.556 3.88 0.00 0.00 4.16
2947 3003 2.058829 CTGTTGTTGGCCACGGTGTC 62.059 60.000 3.88 0.00 0.00 3.67
2948 3004 2.115911 GTTGTTGGCCACGGTGTCA 61.116 57.895 3.88 2.49 0.00 3.58
2949 3005 1.152860 TTGTTGGCCACGGTGTCAT 60.153 52.632 3.88 0.00 0.00 3.06
2950 3006 0.753479 TTGTTGGCCACGGTGTCATT 60.753 50.000 3.88 0.00 0.00 2.57
2951 3007 0.753479 TGTTGGCCACGGTGTCATTT 60.753 50.000 3.88 0.00 0.00 2.32
2952 3008 0.318614 GTTGGCCACGGTGTCATTTG 60.319 55.000 3.88 0.00 0.00 2.32
2953 3009 2.081425 TTGGCCACGGTGTCATTTGC 62.081 55.000 3.88 1.89 0.00 3.68
2954 3010 2.258286 GCCACGGTGTCATTTGCC 59.742 61.111 7.45 0.00 0.00 4.52
2955 3011 2.268076 GCCACGGTGTCATTTGCCT 61.268 57.895 7.45 0.00 0.00 4.75
2956 3012 0.958382 GCCACGGTGTCATTTGCCTA 60.958 55.000 7.45 0.00 0.00 3.93
2957 3013 1.750193 CCACGGTGTCATTTGCCTAT 58.250 50.000 7.45 0.00 0.00 2.57
2958 3014 2.091541 CCACGGTGTCATTTGCCTATT 58.908 47.619 7.45 0.00 0.00 1.73
2959 3015 2.159393 CCACGGTGTCATTTGCCTATTG 60.159 50.000 7.45 0.00 0.00 1.90
2960 3016 2.091541 ACGGTGTCATTTGCCTATTGG 58.908 47.619 0.00 0.00 0.00 3.16
2974 3030 2.203280 TTGGCACTGGACCAACGG 60.203 61.111 0.00 0.00 42.23 4.44
2975 3031 3.050354 TTGGCACTGGACCAACGGT 62.050 57.895 0.00 0.00 42.23 4.83
2976 3032 2.203294 GGCACTGGACCAACGGTT 60.203 61.111 0.00 0.00 35.25 4.44
2977 3033 2.258726 GGCACTGGACCAACGGTTC 61.259 63.158 0.00 0.00 35.25 3.62
2978 3034 1.525077 GCACTGGACCAACGGTTCA 60.525 57.895 0.00 0.00 39.18 3.18
2981 3037 3.236391 TGGACCAACGGTTCAGCT 58.764 55.556 0.00 0.00 36.07 4.24
2982 3038 1.070786 TGGACCAACGGTTCAGCTC 59.929 57.895 0.00 0.00 36.07 4.09
2983 3039 1.070786 GGACCAACGGTTCAGCTCA 59.929 57.895 0.00 0.00 35.25 4.26
2984 3040 0.951040 GGACCAACGGTTCAGCTCAG 60.951 60.000 0.00 0.00 35.25 3.35
2985 3041 1.569479 GACCAACGGTTCAGCTCAGC 61.569 60.000 0.00 0.00 35.25 4.26
2986 3042 2.671177 CCAACGGTTCAGCTCAGCG 61.671 63.158 11.54 11.54 40.95 5.18
2987 3043 2.357517 AACGGTTCAGCTCAGCGG 60.358 61.111 16.23 0.00 39.46 5.52
2992 3048 4.742201 TTCAGCTCAGCGGCCGTC 62.742 66.667 28.70 19.09 0.00 4.79
3004 3060 4.012895 GCCGTCGGTTGTGTGCAG 62.013 66.667 13.94 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 3.452990 TGTATTGGATTCCTTGAGGCGTA 59.547 43.478 3.95 0.00 34.44 4.42
95 96 6.204688 CCACGATTTGGCTACATGTATGTATT 59.795 38.462 5.91 0.00 39.33 1.89
135 136 3.998099 TCTCCTATCGCTCTGAATGTG 57.002 47.619 0.00 0.00 0.00 3.21
150 151 3.523564 TCCCGAATTCAATTCCTTCTCCT 59.476 43.478 6.22 0.00 35.89 3.69
330 333 1.548719 GGGAAAACTCGGGGGAAATTG 59.451 52.381 0.00 0.00 0.00 2.32
348 351 1.826024 CATCTTGAGGACGGAGGGG 59.174 63.158 0.00 0.00 0.00 4.79
438 441 2.869503 ATTGCTGGCGGGAGTTACGG 62.870 60.000 0.00 0.00 0.00 4.02
523 529 2.159517 GGCTGTAAAACTGGCAAGATCG 60.160 50.000 0.00 0.00 41.20 3.69
548 554 1.069500 CCACGAAACCGAAGCGAAAAT 60.069 47.619 0.00 0.00 0.00 1.82
574 580 3.989787 GCAAAACGGCCCACCTGG 61.990 66.667 0.00 0.00 37.09 4.45
626 632 6.942886 TTTTATGGCATTTCATTTCACGTC 57.057 33.333 4.78 0.00 0.00 4.34
630 636 7.066043 GGCAGAATTTTATGGCATTTCATTTCA 59.934 33.333 4.78 0.00 43.46 2.69
631 637 7.281549 AGGCAGAATTTTATGGCATTTCATTTC 59.718 33.333 4.78 3.75 45.99 2.17
632 638 7.114095 AGGCAGAATTTTATGGCATTTCATTT 58.886 30.769 4.78 0.00 45.99 2.32
633 639 6.655930 AGGCAGAATTTTATGGCATTTCATT 58.344 32.000 4.78 1.20 45.99 2.57
634 640 6.243216 AGGCAGAATTTTATGGCATTTCAT 57.757 33.333 4.78 0.00 45.99 2.57
671 677 4.054825 AGCAACGCAAATGGCCGG 62.055 61.111 0.00 0.00 40.31 6.13
823 840 0.814457 CGTGAGAGGTGGAAGAGGAG 59.186 60.000 0.00 0.00 0.00 3.69
842 860 2.682352 GGAAGATCCAAGCAGAAGAAGC 59.318 50.000 0.00 0.00 36.28 3.86
879 897 3.535629 TTGCTCAGCCGTGGGACAG 62.536 63.158 0.00 0.00 41.80 3.51
928 961 5.536538 AGAGATCAGATACCGTAATGCTTGA 59.463 40.000 0.00 0.00 0.00 3.02
937 970 1.339610 GCAGCAGAGATCAGATACCGT 59.660 52.381 0.00 0.00 0.00 4.83
943 976 1.790818 ATGGAGCAGCAGAGATCAGA 58.209 50.000 0.00 0.00 0.00 3.27
974 1007 0.468226 ACGAGCAAGACAAACTCCCA 59.532 50.000 0.00 0.00 0.00 4.37
975 1008 1.531578 GAACGAGCAAGACAAACTCCC 59.468 52.381 0.00 0.00 0.00 4.30
979 1012 0.384353 GCCGAACGAGCAAGACAAAC 60.384 55.000 0.00 0.00 0.00 2.93
995 1028 4.758251 TGTGCCTGTCCATCGCCG 62.758 66.667 0.00 0.00 0.00 6.46
1570 1603 1.111116 TCCTCGTCGAACACCTTGGT 61.111 55.000 0.00 0.00 0.00 3.67
1698 1731 3.834799 CCGAGGGCCTGGTACGAC 61.835 72.222 12.95 0.00 0.00 4.34
1885 1939 4.830765 CCCGCATTTCGCCGGAGA 62.831 66.667 5.05 3.81 41.13 3.71
1994 2048 0.964700 CAGCTGACCTCACTGTCTGA 59.035 55.000 8.42 0.00 36.60 3.27
2016 2070 1.291877 GACGGCTGGTCACATGTCAC 61.292 60.000 0.00 0.00 45.36 3.67
2021 2075 2.261671 GACGACGGCTGGTCACAT 59.738 61.111 0.00 0.00 46.42 3.21
2046 2100 0.179089 ATCTGAGCACATCTGGCGAC 60.179 55.000 0.00 0.00 36.08 5.19
2093 2148 1.812686 ATCCATGCATGCCGATTGCC 61.813 55.000 21.69 0.00 39.39 4.52
2100 2155 1.045407 ACAATCCATCCATGCATGCC 58.955 50.000 21.69 0.00 0.00 4.40
2118 2173 1.475930 GGATGAAGAGCCCTTGCCTAC 60.476 57.143 0.00 0.00 38.69 3.18
2119 2174 0.839946 GGATGAAGAGCCCTTGCCTA 59.160 55.000 0.00 0.00 38.69 3.93
2190 2245 8.785329 AATTGTAACTGAAAAGAAAAGGCAAA 57.215 26.923 0.00 0.00 0.00 3.68
2191 2246 9.308318 GTAATTGTAACTGAAAAGAAAAGGCAA 57.692 29.630 0.00 0.00 0.00 4.52
2192 2247 8.470805 TGTAATTGTAACTGAAAAGAAAAGGCA 58.529 29.630 0.00 0.00 0.00 4.75
2193 2248 8.865590 TGTAATTGTAACTGAAAAGAAAAGGC 57.134 30.769 0.00 0.00 0.00 4.35
2241 2296 2.019984 GGGCTGTTCAGCTAATTCAGG 58.980 52.381 21.46 0.00 34.73 3.86
2264 2319 6.959639 AAGTGTACAGTGGACAAAAATGAT 57.040 33.333 10.53 0.00 0.00 2.45
2760 2816 1.882625 GAGATATGGCGCGCACACA 60.883 57.895 34.42 22.28 0.00 3.72
2761 2817 1.552348 GAGAGATATGGCGCGCACAC 61.552 60.000 34.42 16.64 0.00 3.82
2762 2818 1.300156 GAGAGATATGGCGCGCACA 60.300 57.895 34.42 27.19 0.00 4.57
2763 2819 1.300156 TGAGAGATATGGCGCGCAC 60.300 57.895 34.42 22.27 0.00 5.34
2764 2820 1.300156 GTGAGAGATATGGCGCGCA 60.300 57.895 34.42 19.50 0.00 6.09
2765 2821 1.006805 AGTGAGAGATATGGCGCGC 60.007 57.895 25.94 25.94 0.00 6.86
2766 2822 0.665670 CCAGTGAGAGATATGGCGCG 60.666 60.000 0.00 0.00 0.00 6.86
2767 2823 0.320247 CCCAGTGAGAGATATGGCGC 60.320 60.000 0.00 0.00 0.00 6.53
2768 2824 1.332195 TCCCAGTGAGAGATATGGCG 58.668 55.000 0.00 0.00 0.00 5.69
2769 2825 4.070716 CAAATCCCAGTGAGAGATATGGC 58.929 47.826 0.00 0.00 0.00 4.40
2770 2826 5.303971 GTCAAATCCCAGTGAGAGATATGG 58.696 45.833 0.00 0.00 0.00 2.74
2771 2827 5.303971 GGTCAAATCCCAGTGAGAGATATG 58.696 45.833 0.00 0.00 0.00 1.78
2817 2873 7.868415 AGCTGTTTCTACTACTGTAAAGTTCAG 59.132 37.037 0.00 0.00 38.68 3.02
2833 2889 4.040461 AGCTTAAGTGGTGAGCTGTTTCTA 59.960 41.667 4.02 0.00 44.53 2.10
2834 2890 3.142174 GCTTAAGTGGTGAGCTGTTTCT 58.858 45.455 4.02 0.00 33.72 2.52
2836 2892 3.142174 GAGCTTAAGTGGTGAGCTGTTT 58.858 45.455 4.02 0.00 46.08 2.83
2852 2908 1.237285 ATTGGCAGTTTCGCGAGCTT 61.237 50.000 16.29 0.59 0.00 3.74
2870 2926 5.022122 TCAGCATTATAGGAGCTAGAGCAT 58.978 41.667 4.01 0.00 45.16 3.79
2881 2937 8.668510 ACTATTCAACTGTTCAGCATTATAGG 57.331 34.615 0.00 0.00 0.00 2.57
2889 2945 5.786401 ATTCGACTATTCAACTGTTCAGC 57.214 39.130 0.00 0.00 0.00 4.26
2890 2946 8.376203 CAACTATTCGACTATTCAACTGTTCAG 58.624 37.037 0.00 0.00 0.00 3.02
2891 2947 7.148639 GCAACTATTCGACTATTCAACTGTTCA 60.149 37.037 0.00 0.00 0.00 3.18
2892 2948 7.148639 TGCAACTATTCGACTATTCAACTGTTC 60.149 37.037 0.00 0.00 0.00 3.18
2893 2949 6.649141 TGCAACTATTCGACTATTCAACTGTT 59.351 34.615 0.00 0.00 0.00 3.16
2894 2950 6.163476 TGCAACTATTCGACTATTCAACTGT 58.837 36.000 0.00 0.00 0.00 3.55
2895 2951 6.647212 TGCAACTATTCGACTATTCAACTG 57.353 37.500 0.00 0.00 0.00 3.16
2896 2952 7.667043 TTTGCAACTATTCGACTATTCAACT 57.333 32.000 0.00 0.00 0.00 3.16
2897 2953 7.270579 GGTTTTGCAACTATTCGACTATTCAAC 59.729 37.037 0.00 0.00 32.90 3.18
2898 2954 7.174253 AGGTTTTGCAACTATTCGACTATTCAA 59.826 33.333 0.00 0.00 32.90 2.69
2899 2955 6.653320 AGGTTTTGCAACTATTCGACTATTCA 59.347 34.615 0.00 0.00 32.90 2.57
2900 2956 7.073342 AGGTTTTGCAACTATTCGACTATTC 57.927 36.000 0.00 0.00 32.90 1.75
2901 2957 8.556213 TTAGGTTTTGCAACTATTCGACTATT 57.444 30.769 0.00 0.00 32.90 1.73
2902 2958 8.448615 GTTTAGGTTTTGCAACTATTCGACTAT 58.551 33.333 0.00 0.00 32.90 2.12
2903 2959 7.658575 AGTTTAGGTTTTGCAACTATTCGACTA 59.341 33.333 0.00 0.00 32.90 2.59
2904 2960 6.485648 AGTTTAGGTTTTGCAACTATTCGACT 59.514 34.615 0.00 0.00 32.90 4.18
2905 2961 6.577427 CAGTTTAGGTTTTGCAACTATTCGAC 59.423 38.462 0.00 0.00 32.90 4.20
2906 2962 6.261381 ACAGTTTAGGTTTTGCAACTATTCGA 59.739 34.615 0.00 0.00 32.90 3.71
2907 2963 6.435428 ACAGTTTAGGTTTTGCAACTATTCG 58.565 36.000 0.00 0.00 32.90 3.34
2908 2964 7.704899 ACAACAGTTTAGGTTTTGCAACTATTC 59.295 33.333 0.00 0.00 32.90 1.75
2909 2965 7.552459 ACAACAGTTTAGGTTTTGCAACTATT 58.448 30.769 0.00 0.00 32.90 1.73
2910 2966 7.107639 ACAACAGTTTAGGTTTTGCAACTAT 57.892 32.000 0.00 0.00 32.90 2.12
2911 2967 6.518208 ACAACAGTTTAGGTTTTGCAACTA 57.482 33.333 0.00 0.00 32.90 2.24
2912 2968 5.400066 ACAACAGTTTAGGTTTTGCAACT 57.600 34.783 0.00 0.00 32.90 3.16
2913 2969 5.163903 CCAACAACAGTTTAGGTTTTGCAAC 60.164 40.000 0.00 0.00 0.00 4.17
2914 2970 4.932200 CCAACAACAGTTTAGGTTTTGCAA 59.068 37.500 0.00 0.00 0.00 4.08
2915 2971 4.499183 CCAACAACAGTTTAGGTTTTGCA 58.501 39.130 0.00 0.00 0.00 4.08
2916 2972 3.308595 GCCAACAACAGTTTAGGTTTTGC 59.691 43.478 0.00 0.00 0.00 3.68
2917 2973 3.868661 GGCCAACAACAGTTTAGGTTTTG 59.131 43.478 0.00 0.00 0.00 2.44
2918 2974 3.515901 TGGCCAACAACAGTTTAGGTTTT 59.484 39.130 0.61 0.00 0.00 2.43
2919 2975 3.100671 TGGCCAACAACAGTTTAGGTTT 58.899 40.909 0.61 0.00 0.00 3.27
2920 2976 2.429250 GTGGCCAACAACAGTTTAGGTT 59.571 45.455 7.24 0.00 0.00 3.50
2921 2977 2.028876 GTGGCCAACAACAGTTTAGGT 58.971 47.619 7.24 0.00 0.00 3.08
2922 2978 1.001815 CGTGGCCAACAACAGTTTAGG 60.002 52.381 7.24 0.00 0.00 2.69
2923 2979 1.001815 CCGTGGCCAACAACAGTTTAG 60.002 52.381 7.24 0.00 0.00 1.85
2924 2980 1.025812 CCGTGGCCAACAACAGTTTA 58.974 50.000 7.24 0.00 0.00 2.01
2925 2981 0.968393 ACCGTGGCCAACAACAGTTT 60.968 50.000 7.24 0.00 0.00 2.66
2926 2982 1.379309 ACCGTGGCCAACAACAGTT 60.379 52.632 7.24 0.00 0.00 3.16
2927 2983 2.118404 CACCGTGGCCAACAACAGT 61.118 57.895 7.24 0.00 0.00 3.55
2928 2984 2.058829 GACACCGTGGCCAACAACAG 62.059 60.000 7.24 0.00 0.00 3.16
2929 2985 2.044848 ACACCGTGGCCAACAACA 60.045 55.556 7.24 0.00 0.00 3.33
2930 2986 1.452145 ATGACACCGTGGCCAACAAC 61.452 55.000 7.24 0.00 0.00 3.32
2931 2987 0.753479 AATGACACCGTGGCCAACAA 60.753 50.000 7.24 0.00 0.00 2.83
2932 2988 0.753479 AAATGACACCGTGGCCAACA 60.753 50.000 7.24 1.46 0.00 3.33
2933 2989 0.318614 CAAATGACACCGTGGCCAAC 60.319 55.000 7.24 0.15 0.00 3.77
2934 2990 2.037053 CAAATGACACCGTGGCCAA 58.963 52.632 7.24 0.00 0.00 4.52
2935 2991 2.560119 GCAAATGACACCGTGGCCA 61.560 57.895 0.00 0.00 0.00 5.36
2936 2992 2.258286 GCAAATGACACCGTGGCC 59.742 61.111 0.75 0.00 0.00 5.36
2937 2993 0.958382 TAGGCAAATGACACCGTGGC 60.958 55.000 3.03 0.00 36.84 5.01
2938 2994 1.750193 ATAGGCAAATGACACCGTGG 58.250 50.000 3.03 0.00 0.00 4.94
2939 2995 2.159393 CCAATAGGCAAATGACACCGTG 60.159 50.000 0.00 0.00 0.00 4.94
2940 2996 2.091541 CCAATAGGCAAATGACACCGT 58.908 47.619 0.00 0.00 0.00 4.83
2941 2997 2.849880 CCAATAGGCAAATGACACCG 57.150 50.000 0.00 0.00 0.00 4.94
2953 3009 1.463674 GTTGGTCCAGTGCCAATAGG 58.536 55.000 5.62 0.00 46.25 2.57
2954 3010 1.086696 CGTTGGTCCAGTGCCAATAG 58.913 55.000 5.62 1.06 46.25 1.73
2955 3011 0.322098 CCGTTGGTCCAGTGCCAATA 60.322 55.000 5.62 0.00 46.25 1.90
2956 3012 1.603455 CCGTTGGTCCAGTGCCAAT 60.603 57.895 5.62 0.00 46.25 3.16
2957 3013 2.203280 CCGTTGGTCCAGTGCCAA 60.203 61.111 0.00 0.00 43.04 4.52
2958 3014 2.951475 GAACCGTTGGTCCAGTGCCA 62.951 60.000 0.00 0.00 33.12 4.92
2959 3015 2.203294 AACCGTTGGTCCAGTGCC 60.203 61.111 0.00 0.00 33.12 5.01
2960 3016 1.507141 CTGAACCGTTGGTCCAGTGC 61.507 60.000 0.00 0.00 33.12 4.40
2961 3017 1.507141 GCTGAACCGTTGGTCCAGTG 61.507 60.000 4.11 0.00 33.12 3.66
2962 3018 1.227853 GCTGAACCGTTGGTCCAGT 60.228 57.895 4.11 0.00 33.12 4.00
2963 3019 0.951040 GAGCTGAACCGTTGGTCCAG 60.951 60.000 0.00 0.00 33.12 3.86
2964 3020 1.070786 GAGCTGAACCGTTGGTCCA 59.929 57.895 0.00 0.00 33.12 4.02
2965 3021 0.951040 CTGAGCTGAACCGTTGGTCC 60.951 60.000 0.00 0.00 33.12 4.46
2966 3022 1.569479 GCTGAGCTGAACCGTTGGTC 61.569 60.000 0.00 0.00 33.12 4.02
2967 3023 1.598130 GCTGAGCTGAACCGTTGGT 60.598 57.895 0.00 0.00 37.65 3.67
2968 3024 2.671177 CGCTGAGCTGAACCGTTGG 61.671 63.158 1.78 0.00 0.00 3.77
2969 3025 2.671177 CCGCTGAGCTGAACCGTTG 61.671 63.158 1.78 0.00 0.00 4.10
2970 3026 2.357517 CCGCTGAGCTGAACCGTT 60.358 61.111 1.78 0.00 0.00 4.44
2975 3031 4.742201 GACGGCCGCTGAGCTGAA 62.742 66.667 28.58 0.00 42.00 3.02
2987 3043 4.012895 CTGCACACAACCGACGGC 62.013 66.667 15.39 0.00 0.00 5.68


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.